[ensembl-dev] [EnsemblGenomes] $NCBI_taxon_adaptor->fetch_node_by_name() not working for some divisions

[Giuseppe Gallone]

Hi thanks for your reply. Unfortunately the inconsistency is there when
I use the pan taxonomic db as well. If a taxon object is not returned
for a scientific name in its db, it won't be returned if the pan
homology db is set instead.

Regards
G.

On 25/09/10 14:21, Daniel Hughes wrote:
> Perhaps use pan compara and not division specific DBs:
>
> mysql> use ensembl_compara_pan_homology_6_59
> Database changed
> mysql> select * from ncbi_taxa_name where name like 'Aspergillus
> nidulans' \G
> *************************** 1. row ***************************
>    taxon_id: 162425
>        name: Aspergillus nidulans
> name_class: genbank anamorph
> 1 row in set (0.30 sec)
>
> mysql> use ensembl_compara_fungi_6_59
> Database changed
> mysql> select * from ncbi_taxa_node;
> Empty set (0.04 sec)
>
> dan.
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
> -------------------------------------------------------------------------------------
> dsth at cantab.net <mailto:dsth at cantab.net>
> dsth at cpan.org <mailto:dsth at cpan.org>
>
>
> 2010/9/25 Daniel Hughes <dsth at ebi.ac.uk <mailto:dsth at ebi.ac.uk>>
>
>     Not very familiar with Compara, but perhaps:
>
>     mysql> use aspergillus_nidulans_core_6_59_6e
>     Database changed
>     mysql> select meta_value from meta where meta_key =
>     'species.taxonomy_id' \G
>     *************************** 1. row ***************************
>     meta_value: 162425
>     1 row in set (0.09 sec)
>
>     mysql> use ensembl_compara_metazoa_6_59
>     Database changed
>     mysql> select * from ncbi_taxa_name where name like 'Aspergillus
>     nidulans' \G
>     *************************** 1. row ***************************
>        taxon_id: 162425
>            name: Aspergillus nidulans
>     name_class: genbank anamorph
>     1 row in set (0.10 sec)
>
>     mysql> use ensembl_compara_fungi_6_59
>     Database changed
>     mysql> select * from ncbi_taxa_name where name like 'Aspergillus
>     nidulans' \G
>     Empty set (0.12 sec)
>
>     Dan
>
>     Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>     -------------------------------------------------------------------------------------
>     dsth at cantab.net <mailto:dsth at cantab.net>
>     dsth at cpan.org <mailto:dsth at cpan.org>
>
>

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